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- PDB-1jn0: Crystal structure of the non-regulatory A4 isoform of spinach chl... -

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Basic information

Entry
Database: PDB / ID: 1jn0
TitleCrystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP
ComponentsGLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / PROTEIN-NADP COMPLEX / NADPH
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / chloroplast / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFermani, S. / Ripamonti, A. / Sabatino, P. / Zanotti, G. / Scagliarini, S. / Sparla, F. / Trost, P. / Pupillo, P.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the non-regulatory A(4 )isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP.
Authors: Fermani, S. / Ripamonti, A. / Sabatino, P. / Zanotti, G. / Scagliarini, S. / Sparla, F. / Trost, P. / Pupillo, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray study of chloroplast glyceraldehyde-3-phosphate dehydrogenase
Authors: Sabatino, P. / Fermani, S. / Ripamonti, A. / Cassetta, A. / Scagliarini, S. / Trost, P.
#2: Journal: J.Exp.Bot. / Year: 1998
Title: The non-regulatory isoform of NADP(H)-glyceraldehyde-3-phosphate dehydrogenase from spinach chloroplasts
Authors: Scagliarini, S. / Trost, P. / Pupillo, P.
#3: Journal: Biochim.Biophys.Acta / Year: 1990
Title: Chloroplast glyceraldehyde-3-phosphate dehydrogenase (NADP): amino acid sequence of the subunits from isoenzyme I and structural relationship with isoenzyme II.
Authors: Ferri, G. / Stoppini, M. / Meloni, M. / Zapponi, M.C. / Iadarola, P.
History
DepositionJul 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,84912
Polymers108,0363
Non-polymers2,8139
Water3,819212
1
A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,79916
Polymers144,0494
Non-polymers3,75012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+3/2,-y+3/2,z1
Buried area20500 Å2
ΔGint-259 kcal/mol
Surface area42560 Å2
MethodPISA, PQS
2
O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules

O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules

O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules

O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,79916
Polymers144,0494
Non-polymers3,75012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area20470 Å2
ΔGint-253 kcal/mol
Surface area42300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.249, 182.184, 106.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
DetailsOne tetramer with crystallographic 222 symmetry is generated from the monomer O by the operations -x, -y, z and -x, y, -z and x, -y, -z another similar tetramer with a crystallographic 2 symmetry is generated from the dimer O'R' by the operation 1/2-x, 1/2-y, z.

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Components

#1: Protein GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A / E.C.1.2.1.13 / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A /


Mass: 36012.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: tetramer GAPDH 2 / Source: (natural) Spinacia oleracea (spinach) / Cellular location: CHLOROPLAST
References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulphate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7
Details: Sabatino, P., (1999) Acta Crystallogr., Sect.D, 55, 566.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMpotassium phosphate1droppH7
31 mMNADP+1drop
41.2-1.5 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 3, 1999
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→69 Å / Num. all: 28763 / Num. obs: 26762 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Rsym value: 0.132 / Net I/σ(I): 7.11
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.499 / Num. unique all: 2308 / Rsym value: 0.437 / % possible all: 80.8
Reflection
*PLUS
% possible obs: 93 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DBV

2dbv


Resolution: 3→49.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4360318.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Chains A and B correspond to O' and R' respectively. Arg23, Asp70 and Ala337 were deleted from the model because the electron density did not allow their positioning. Each monomer is numbered 1 to 337.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1841 6.9 %RANDOM
Rwork0.213 ---
obs0.213 26750 93 %-
all-28763 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1735 Å2 / ksol: 0.37947 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1-28.74 Å20 Å20 Å2
2---5.14 Å20 Å2
3----23.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7563 0 174 212 7949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d5.26
X-RAY DIFFRACTIONc_mcbond_it3.611.5
X-RAY DIFFRACTIONc_mcangle_it5.612
X-RAY DIFFRACTIONc_scbond_it6.192
X-RAY DIFFRACTIONc_scangle_it8.822.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 285 7.4 %
Rwork0.32 3579 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NDP.PARAMNDP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 69 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg5.26
X-RAY DIFFRACTIONc_mcbond_it3.611.5
X-RAY DIFFRACTIONc_scbond_it6.192
X-RAY DIFFRACTIONc_mcangle_it5.612
X-RAY DIFFRACTIONc_scangle_it8.822.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.386 / % reflection Rfree: 7.4 % / Rfactor Rwork: 0.32

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